HEADER TRANSFERASE 15-SEP-15 5APG TITLE STRUCTURE OF THE SAM-DEPENDENT RRNA:ACP-TRANSFERASE TSR3 FROM TITLE 2 VULCANISAETA DISTRIBUTA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TSR3; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 2.5.1.-; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CONTAINING SELENOMETHIONINE INSTEAD OF METHIONINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VULCANISAETA DISTRIBUTA; SOURCE 3 ORGANISM_TAXID: 572478; SOURCE 4 STRAIN: DSM 14429; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET11 KEYWDS TRANSFERASE, S-ADENOSYLMETHIONINE, S-ADENOSYLMETHIONINE DEPENDENT 3- KEYWDS 2 AMINO-3-CARBOXYPROPYL TRANSFERASE, RRNA, PSEUDOURIDINE, SAM, SPOUT- KEYWDS 3 FOLD EXPDTA X-RAY DIFFRACTION AUTHOR J.P.WURM,C.IMMER,D.POGORYELOV,B.MEYER,P.KOETTER,K.-D.ENTIAN, AUTHOR 2 J.WOEHNERT REVDAT 3 20-NOV-24 5APG 1 REMARK LINK REVDAT 2 01-JUN-16 5APG 1 JRNL REVDAT 1 27-APR-16 5APG 0 JRNL AUTH K.-D.ENTIAN,C.IMMER,P.KOETTER,D.LAFONTAINE,M.BRITTER, JRNL AUTH 2 D.POGORYELOV,S.SHARMA,J.WOHNERT,J.P.WURM JRNL TITL RIBOSOME BIOGENESIS FACTOR TSR3 IS THE AMINOCARBOXYPROPYL JRNL TITL 2 TRANSFERASE RESPONSIBLE FOR 18S RRNA HYPERMODIFICATION IN JRNL TITL 3 YEAST AND HUMANS JRNL REF NUCLEIC ACIDS RES. V. 44 4304 2016 JRNL REFN ISSN 0305-1048 JRNL PMID 27084949 JRNL DOI 10.1093/NAR/GKW244 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 107486 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 10562 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.2199 - 4.9684 1.00 6726 353 0.1764 0.1862 REMARK 3 2 4.9684 - 3.9447 1.00 6614 346 0.1430 0.1425 REMARK 3 3 3.9447 - 3.4464 1.00 6759 357 0.1574 0.1684 REMARK 3 4 3.4464 - 3.1315 1.00 6625 356 0.1821 0.2005 REMARK 3 5 3.1315 - 2.9071 1.00 6664 349 0.1918 0.1896 REMARK 3 6 2.9071 - 2.7358 1.00 6772 361 0.1818 0.1858 REMARK 3 7 2.7358 - 2.5988 1.00 6675 350 0.1902 0.2038 REMARK 3 8 2.5988 - 2.4857 1.00 6663 351 0.1843 0.1854 REMARK 3 9 2.4857 - 2.3900 1.00 6656 352 0.1781 0.1973 REMARK 3 10 2.3900 - 2.3075 1.00 6650 352 0.1897 0.1979 REMARK 3 11 2.3075 - 2.2354 1.00 6699 352 0.1793 0.1953 REMARK 3 12 2.2354 - 2.1715 1.00 6782 354 0.1863 0.2059 REMARK 3 13 2.1715 - 2.1143 1.00 6709 358 0.1886 0.2174 REMARK 3 14 2.1143 - 2.0627 1.00 6589 346 0.2034 0.2291 REMARK 3 15 2.0627 - 2.0159 1.00 6741 355 0.1927 0.2230 REMARK 3 16 2.0159 - 1.9730 1.00 6678 350 0.2147 0.2254 REMARK 3 17 1.9730 - 1.9335 1.00 6656 350 0.2287 0.2368 REMARK 3 18 1.9335 - 1.8970 1.00 6665 347 0.2478 0.2414 REMARK 3 19 1.8970 - 1.8631 1.00 6757 354 0.2351 0.2516 REMARK 3 20 1.8631 - 1.8315 1.00 6754 357 0.2393 0.2333 REMARK 3 21 1.8315 - 1.8020 1.00 6633 351 0.2443 0.2475 REMARK 3 22 1.8020 - 1.7743 1.00 6678 348 0.2597 0.2984 REMARK 3 23 1.7743 - 1.7482 1.00 6690 355 0.2663 0.2679 REMARK 3 24 1.7482 - 1.7236 1.00 6581 346 0.2761 0.2951 REMARK 3 25 1.7236 - 1.7003 1.00 6837 359 0.2778 0.2854 REMARK 3 26 1.7003 - 1.6782 1.00 6568 343 0.2998 0.3146 REMARK 3 27 1.6782 - 1.6572 1.00 6694 353 0.3040 0.3147 REMARK 3 28 1.6572 - 1.6372 1.00 6693 351 0.3044 0.2976 REMARK 3 29 1.6372 - 1.6182 1.00 6780 357 0.3333 0.3515 REMARK 3 30 1.6182 - 1.6000 1.00 6625 349 0.3395 0.3524 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 4584 REMARK 3 ANGLE : 1.094 6230 REMARK 3 CHIRALITY : 0.353 713 REMARK 3 PLANARITY : 0.005 775 REMARK 3 DIHEDRAL : 13.895 1724 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5APG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1290065003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107521 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 39.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 27.40 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.7300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 26.00 REMARK 200 R MERGE FOR SHELL (I) : 1.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX AUTOSOL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 57.97500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.48500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.97500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.48500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C2030 LIES ON A SPECIAL POSITION. REMARK 375 HOH C2073 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 185 REMARK 465 ASP B 185 REMARK 465 ASP C 185 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 12 CG CD OE1 NE2 REMARK 470 ASP A 13 CG OD1 OD2 REMARK 470 ARG A 16 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 36 CG CD CE NZ REMARK 470 GLN B 12 CG CD OE1 NE2 REMARK 470 ASP B 13 CG OD1 OD2 REMARK 470 ARG B 16 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 36 CG CD CE NZ REMARK 470 GLN C 12 CG CD OE1 NE2 REMARK 470 ASP C 13 CG OD1 OD2 REMARK 470 ARG C 16 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 36 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2045 O HOH A 2185 1.84 REMARK 500 O HOH C 2094 O HOH C 2171 1.88 REMARK 500 O HOH A 2049 O HOH A 2050 1.94 REMARK 500 O HOH B 2112 O HOH B 2113 1.97 REMARK 500 NH2 ARG C 179 O HOH C 2166 2.00 REMARK 500 O ILE C 84 O HOH C 2104 2.02 REMARK 500 O HOH B 2046 O HOH B 2172 2.07 REMARK 500 O HOH A 2082 O HOH A 2084 2.08 REMARK 500 O HOH B 2086 O HOH B 2087 2.09 REMARK 500 O HOH A 2089 O HOH A 2090 2.10 REMARK 500 NE2 GLN C 147 O HOH C 2146 2.12 REMARK 500 OH TYR A 104 O HOH A 2129 2.13 REMARK 500 O HOH B 2073 O HOH B 2133 2.14 REMARK 500 O HOH C 2025 O HOH C 2054 2.15 REMARK 500 O HOH C 2010 O HOH C 2047 2.17 REMARK 500 O HOH C 2104 O HOH C 2105 2.17 REMARK 500 O HOH A 2011 O HOH A 2050 2.18 REMARK 500 O HOH B 2103 O HOH B 2173 2.18 REMARK 500 O HOH A 2144 O HOH A 2145 2.19 REMARK 500 OH TYR C 104 O HOH C 2121 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 2176 O HOH C 2088 4748 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 11 75.10 -68.29 REMARK 500 TYR A 108 -40.29 75.18 REMARK 500 GLN B 12 71.46 -117.31 REMARK 500 TYR B 108 -39.74 77.70 REMARK 500 GLN C 12 68.94 -118.16 REMARK 500 TYR C 108 -41.72 76.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2035 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH B2035 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH B2074 DISTANCE = 5.90 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EEM B 1185 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EEM A 1185 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EEM C 1185 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 1186 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 1186 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 1187 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AP8 RELATED DB: PDB REMARK 900 STRUCTURE OF THE SAM-DEPENDENT RRNA:ACP-TRANSFERASE TSR3 FROM S. REMARK 900 SOLFATARICUS DBREF 5APG A 1 185 UNP E1QU22 E1QU22_VULDI 1 185 DBREF 5APG B 1 185 UNP E1QU22 E1QU22_VULDI 1 185 DBREF 5APG C 1 185 UNP E1QU22 E1QU22_VULDI 1 185 SEQRES 1 A 185 MSE ILE PRO ARG VAL PHE ILE TYR ARG LEU PRO GLN ASP SEQRES 2 A 185 ASP PRO ARG LYS ASN THR ALA ILE LYS LEU VAL ARG PHE SEQRES 3 A 185 GLY PHE ALA GLN LEU VAL ASP SER ILE LYS ALA LEU PRO SEQRES 4 A 185 SER GLY SER ILE ILE LEU ASP PRO THR VAL LYS THR PRO SEQRES 5 A 185 LEU THR PRO SER ASP ARG VAL ILE ALA GLU SER ARG GLY SEQRES 6 A 185 LEU SER LEU ILE ASP CYS SER TRP LYS ARG ALA VAL ASP SEQRES 7 A 185 VAL HIS THR LYS PHE ILE ARG GLY LYS PHE ILE ARG ARG SEQRES 8 A 185 ARG LEU PRO LEU LEU ILE ALA ALA ASN PRO THR HIS TYR SEQRES 9 A 185 GLY LYS PRO TYR ILE LEU SER THR ILE GLU ALA VAL ALA SEQRES 10 A 185 ALA ALA LEU TYR ILE MSE GLY PHE LYS ASP GLU ALA MSE SEQRES 11 A 185 GLU VAL LEU ARG LEU TYR LYS TRP GLY PRO ASN PHE ILE SEQRES 12 A 185 ILE ILE ASN GLN LYS TYR LEU GLU ARG TYR ALA ALA GLY SEQRES 13 A 185 ASP LEU SER PRO GLU ARG GLU LEU LEU GLY VAL ASP ASP SEQRES 14 A 185 VAL ASP ASN GLY LEU GLU GLN LEU MSE ARG VAL LEU THR SEQRES 15 A 185 ASN GLY ASP SEQRES 1 B 185 MSE ILE PRO ARG VAL PHE ILE TYR ARG LEU PRO GLN ASP SEQRES 2 B 185 ASP PRO ARG LYS ASN THR ALA ILE LYS LEU VAL ARG PHE SEQRES 3 B 185 GLY PHE ALA GLN LEU VAL ASP SER ILE LYS ALA LEU PRO SEQRES 4 B 185 SER GLY SER ILE ILE LEU ASP PRO THR VAL LYS THR PRO SEQRES 5 B 185 LEU THR PRO SER ASP ARG VAL ILE ALA GLU SER ARG GLY SEQRES 6 B 185 LEU SER LEU ILE ASP CYS SER TRP LYS ARG ALA VAL ASP SEQRES 7 B 185 VAL HIS THR LYS PHE ILE ARG GLY LYS PHE ILE ARG ARG SEQRES 8 B 185 ARG LEU PRO LEU LEU ILE ALA ALA ASN PRO THR HIS TYR SEQRES 9 B 185 GLY LYS PRO TYR ILE LEU SER THR ILE GLU ALA VAL ALA SEQRES 10 B 185 ALA ALA LEU TYR ILE MSE GLY PHE LYS ASP GLU ALA MSE SEQRES 11 B 185 GLU VAL LEU ARG LEU TYR LYS TRP GLY PRO ASN PHE ILE SEQRES 12 B 185 ILE ILE ASN GLN LYS TYR LEU GLU ARG TYR ALA ALA GLY SEQRES 13 B 185 ASP LEU SER PRO GLU ARG GLU LEU LEU GLY VAL ASP ASP SEQRES 14 B 185 VAL ASP ASN GLY LEU GLU GLN LEU MSE ARG VAL LEU THR SEQRES 15 B 185 ASN GLY ASP SEQRES 1 C 185 MSE ILE PRO ARG VAL PHE ILE TYR ARG LEU PRO GLN ASP SEQRES 2 C 185 ASP PRO ARG LYS ASN THR ALA ILE LYS LEU VAL ARG PHE SEQRES 3 C 185 GLY PHE ALA GLN LEU VAL ASP SER ILE LYS ALA LEU PRO SEQRES 4 C 185 SER GLY SER ILE ILE LEU ASP PRO THR VAL LYS THR PRO SEQRES 5 C 185 LEU THR PRO SER ASP ARG VAL ILE ALA GLU SER ARG GLY SEQRES 6 C 185 LEU SER LEU ILE ASP CYS SER TRP LYS ARG ALA VAL ASP SEQRES 7 C 185 VAL HIS THR LYS PHE ILE ARG GLY LYS PHE ILE ARG ARG SEQRES 8 C 185 ARG LEU PRO LEU LEU ILE ALA ALA ASN PRO THR HIS TYR SEQRES 9 C 185 GLY LYS PRO TYR ILE LEU SER THR ILE GLU ALA VAL ALA SEQRES 10 C 185 ALA ALA LEU TYR ILE MSE GLY PHE LYS ASP GLU ALA MSE SEQRES 11 C 185 GLU VAL LEU ARG LEU TYR LYS TRP GLY PRO ASN PHE ILE SEQRES 12 C 185 ILE ILE ASN GLN LYS TYR LEU GLU ARG TYR ALA ALA GLY SEQRES 13 C 185 ASP LEU SER PRO GLU ARG GLU LEU LEU GLY VAL ASP ASP SEQRES 14 C 185 VAL ASP ASN GLY LEU GLU GLN LEU MSE ARG VAL LEU THR SEQRES 15 C 185 ASN GLY ASP MODRES 5APG MSE A 1 MET SELENOMETHIONINE MODRES 5APG MSE A 123 MET SELENOMETHIONINE MODRES 5APG MSE A 130 MET SELENOMETHIONINE MODRES 5APG MSE A 178 MET SELENOMETHIONINE MODRES 5APG MSE B 1 MET SELENOMETHIONINE MODRES 5APG MSE B 123 MET SELENOMETHIONINE MODRES 5APG MSE B 130 MET SELENOMETHIONINE MODRES 5APG MSE B 178 MET SELENOMETHIONINE MODRES 5APG MSE C 1 MET SELENOMETHIONINE MODRES 5APG MSE C 123 MET SELENOMETHIONINE MODRES 5APG MSE C 130 MET SELENOMETHIONINE MODRES 5APG MSE C 178 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 123 8 HET MSE A 130 8 HET MSE A 178 8 HET MSE B 1 8 HET MSE B 123 8 HET MSE B 130 8 HET MSE B 178 8 HET MSE C 1 8 HET MSE C 123 8 HET MSE C 130 8 HET MSE C 178 8 HET EEM A1185 27 HET MES A1186 12 HET MES A1187 12 HET EEM B1185 27 HET MES B1186 12 HET EEM C1185 27 HETNAM MSE SELENOMETHIONINE HETNAM EEM [(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5- HETNAM 2 EEM (6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]- HETNAM 3 EEM METHYL-SELANIUM HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN EEM SE-ADENOSYLSELENOMETHIONINE FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 4 EEM 3(C15 H23 N6 O5 SE 1+) FORMUL 5 MES 3(C6 H13 N O4 S) FORMUL 10 HOH *539(H2 O) HELIX 1 1 ASN A 18 PHE A 26 1 9 HELIX 2 2 SER A 34 LEU A 38 5 5 HELIX 3 3 THR A 54 SER A 56 5 3 HELIX 4 4 ASP A 57 ARG A 64 1 8 HELIX 5 5 SER A 72 ILE A 84 1 13 HELIX 6 6 SER A 111 MSE A 123 1 13 HELIX 7 7 PHE A 125 ARG A 134 1 10 HELIX 8 8 PRO A 140 ALA A 154 1 15 HELIX 9 9 SER A 159 GLY A 166 1 8 HELIX 10 10 ASP A 169 ASN A 183 1 15 HELIX 11 11 ASP B 14 LYS B 17 5 4 HELIX 12 12 ASN B 18 PHE B 26 1 9 HELIX 13 13 SER B 34 LEU B 38 5 5 HELIX 14 14 THR B 54 SER B 56 5 3 HELIX 15 15 ASP B 57 ARG B 64 1 8 HELIX 16 16 SER B 72 ILE B 84 1 13 HELIX 17 17 SER B 111 MSE B 123 1 13 HELIX 18 18 PHE B 125 ARG B 134 1 10 HELIX 19 19 GLY B 139 ASN B 146 1 8 HELIX 20 20 ASN B 146 ALA B 154 1 9 HELIX 21 21 SER B 159 GLY B 166 1 8 HELIX 22 22 ASP B 169 ASN B 183 1 15 HELIX 23 23 ASN C 18 PHE C 26 1 9 HELIX 24 24 SER C 34 LEU C 38 5 5 HELIX 25 25 THR C 54 SER C 56 5 3 HELIX 26 26 ASP C 57 ARG C 64 1 8 HELIX 27 27 SER C 72 ILE C 84 1 13 HELIX 28 28 SER C 111 MSE C 123 1 13 HELIX 29 29 PHE C 125 ARG C 134 1 10 HELIX 30 30 TRP C 138 ASN C 146 1 9 HELIX 31 31 ASN C 146 ALA C 154 1 9 HELIX 32 32 SER C 159 GLY C 166 1 8 HELIX 33 33 ASP C 169 ASN C 183 1 15 SHEET 1 AA 5 GLN A 30 VAL A 32 0 SHEET 2 AA 5 VAL A 5 ARG A 9 1 O VAL A 5 N GLN A 30 SHEET 3 AA 5 LEU A 66 ASP A 70 1 O LEU A 66 N PHE A 6 SHEET 4 AA 5 ILE A 43 LEU A 45 1 O ILE A 43 N SER A 67 SHEET 5 AA 5 ILE A 89 ARG A 91 1 O ILE A 89 N ILE A 44 SHEET 1 BA 5 GLN B 30 VAL B 32 0 SHEET 2 BA 5 VAL B 5 ARG B 9 1 O VAL B 5 N GLN B 30 SHEET 3 BA 5 LEU B 66 ASP B 70 1 O LEU B 66 N PHE B 6 SHEET 4 BA 5 ILE B 43 LEU B 45 1 O ILE B 43 N SER B 67 SHEET 5 BA 5 ILE B 89 ARG B 91 1 O ILE B 89 N ILE B 44 SHEET 1 CA 5 GLN C 30 VAL C 32 0 SHEET 2 CA 5 VAL C 5 ARG C 9 1 O VAL C 5 N GLN C 30 SHEET 3 CA 5 LEU C 66 ASP C 70 1 O LEU C 66 N PHE C 6 SHEET 4 CA 5 ILE C 43 LEU C 45 1 O ILE C 43 N SER C 67 SHEET 5 CA 5 ILE C 89 ARG C 91 1 O ILE C 89 N ILE C 44 LINK C MSE A 1 N ILE A 2 1555 1555 1.33 LINK C ILE A 122 N MSE A 123 1555 1555 1.33 LINK C MSE A 123 N GLY A 124 1555 1555 1.33 LINK C ALA A 129 N MSE A 130 1555 1555 1.33 LINK C MSE A 130 N GLU A 131 1555 1555 1.33 LINK C LEU A 177 N MSE A 178 1555 1555 1.33 LINK C MSE A 178 N ARG A 179 1555 1555 1.33 LINK C MSE B 1 N ILE B 2 1555 1555 1.33 LINK C ILE B 122 N MSE B 123 1555 1555 1.33 LINK C MSE B 123 N GLY B 124 1555 1555 1.33 LINK C ALA B 129 N MSE B 130 1555 1555 1.33 LINK C MSE B 130 N GLU B 131 1555 1555 1.33 LINK C LEU B 177 N MSE B 178 1555 1555 1.33 LINK C MSE B 178 N ARG B 179 1555 1555 1.33 LINK C MSE C 1 N ILE C 2 1555 1555 1.33 LINK C ILE C 122 N MSE C 123 1555 1555 1.33 LINK C MSE C 123 N GLY C 124 1555 1555 1.33 LINK C ALA C 129 N MSE C 130 1555 1555 1.33 LINK C MSE C 130 N GLU C 131 1555 1555 1.33 LINK C LEU C 177 N MSE C 178 1555 1555 1.33 LINK C MSE C 178 N ARG C 179 1555 1555 1.33 SITE 1 AC1 17 ASN B 18 THR B 19 LEU B 45 PRO B 47 SITE 2 AC1 17 ILE B 69 ASP B 70 CYS B 71 TRP B 73 SITE 3 AC1 17 HIS B 80 LEU B 93 TYR B 108 LEU B 110 SITE 4 AC1 17 SER B 111 THR B 112 ALA B 115 HOH B2026 SITE 5 AC1 17 HOH B2067 SITE 1 AC2 17 ASN A 18 THR A 19 LEU A 45 PRO A 47 SITE 2 AC2 17 LEU A 68 ILE A 69 ASP A 70 CYS A 71 SITE 3 AC2 17 TRP A 73 HIS A 80 LEU A 93 TYR A 108 SITE 4 AC2 17 LEU A 110 SER A 111 THR A 112 ALA A 115 SITE 5 AC2 17 HOH A2067 SITE 1 AC3 18 ASN C 18 THR C 19 LEU C 45 PRO C 47 SITE 2 AC3 18 LEU C 68 ILE C 69 ASP C 70 CYS C 71 SITE 3 AC3 18 TRP C 73 HIS C 80 LEU C 93 TYR C 108 SITE 4 AC3 18 LEU C 110 SER C 111 THR C 112 ALA C 115 SITE 5 AC3 18 HOH C2028 HOH C2061 SITE 1 AC4 10 GLU A 163 GLY A 166 VAL A 167 ASP A 168 SITE 2 AC4 10 HOH A2172 HOH A2187 LYS C 22 LEU C 135 SITE 3 AC4 10 TYR C 136 LYS C 137 SITE 1 AC5 6 LYS B 22 LEU B 135 TYR B 136 LYS B 137 SITE 2 AC5 6 HOH B2142 HOH B2174 SITE 1 AC6 10 LYS A 22 LEU A 135 TYR A 136 LYS A 137 SITE 2 AC6 10 ARG B 162 GLU B 163 GLY B 166 VAL B 167 SITE 3 AC6 10 ASP B 168 HOH B2163 CRYST1 115.950 66.970 106.420 90.00 89.99 90.00 C 1 2 1 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008624 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009397 0.00000 HETATM 1 N MSE A 1 152.550 -12.696 100.038 1.00 45.50 N HETATM 2 CA MSE A 1 151.403 -13.337 99.407 1.00 45.33 C HETATM 3 C MSE A 1 150.401 -13.800 100.454 1.00 38.45 C HETATM 4 O MSE A 1 150.722 -14.630 101.305 1.00 40.85 O HETATM 5 CB MSE A 1 151.851 -14.523 98.550 1.00 42.51 C HETATM 6 CG MSE A 1 150.708 -15.271 97.876 1.00 48.45 C HETATM 7 SE MSE A 1 149.835 -14.226 96.469 1.00 96.18 SE HETATM 8 CE MSE A 1 148.764 -15.643 95.660 1.00 58.26 C